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Increasing demands for efficient and versatile chemical reactions have prompted innovations in enzyme engineering. A major challenge in engineering α-ketoglutarate-dependent oxygenases is to develop a rational strategy which can be widely used for directly evolving the desired mutant to generate new products. Herein, we report a strategy for rational redesign of a model enzyme, 4-hydroxyphenylpyruvate dioxygenase (HPPD), based on quantum mechanics/molecular mechanics (QM/MM) calculation and molecular dynamic simulations. This strategy enriched our understanding of the HPPD catalytic reaction pathway and led to the discovery of a series of HPPD mutants producing hydroxyphenylacetate (HPA) as the alternative product other than the native product homogentisate. The predicted HPPD-Fe(IV)═O-HPA intermediate was further confirmed by the crystal structure of HPPD/S267W complexed with HPA. These findings not only provide a good understanding of the structure-function relationship of HPPD but also demonstrate a generally applicable platform for the development of biocatalysts.
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http://dx.doi.org/10.1021/jacs.1c06227 | DOI Listing |
Bioresour Technol
September 2025
State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Fo
Recombinant proteins have been widely applied in the food, biomedical, and scientific fields. Prokaryotic expression systems are preferred platforms for recombinant protein production due to their rapid growth and high protein yields. Nevertheless, disparities between recombinant expression environment and native physiological conditions frequently result in protein misfolding, leading to aggregation into non-functional inclusion bodies or proteolytic degradation.
View Article and Find Full Text PDFACS Synth Biol
September 2025
Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
Achieving efficient enzyme catalysis under extreme pH conditions remains a major challenge in biocatalysis and synthetic biology. To address this, we present an enzyme engineering strategy that integrates rational redesign of catalytic residues with directed evolution to enable robust enzyme function at alkaline pH. The core principle involves replacing the conserved general base with an ionizable residue of higher intrinsic p, shifting the proton transfer mechanism from carboxylate- to phenolate-mediated catalysis.
View Article and Find Full Text PDFSpectrochim Acta A Mol Biomol Spectrosc
August 2025
Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China. Electronic address:
Early and accurate cancer diagnosis is essential for reducing cancer-related mortality, and miRNA-21 has emerged as a critical biomarker for the early detection of various malignancies In this study, we developed a novel fluorescence biosensor, termed the MXene-SNA-Cas12a, that enables direct and amplification-free detection of miRNA-21 by integrating the CRISPR/Cas12a system with a chimeric split nucleic acid (SNA) activator and MXene-assisted fluorescence modulation. Specifically, a split activator comprising S12 ssDNA hybridized with miRNA-21 was employed to activate the trans-cleavage activity of Cas12a, effectively overcoming the system's inherent limitation in RNA recognition. Simultaneously, MXene nanosheets served as efficient quenchers by adsorbing FAM-labeled ssDNA reporters through non-covalent interactions and facilitating target-induced strand release, enabling a robust fluorescence "on/off" mechanism.
View Article and Find Full Text PDFEBioMedicine
August 2025
Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Beijing Life Science Academy, Beijing, 102209, China; University of Chinese Academy of Sciences, Beijing, 101408, China. Electronic address:
Background: Respiratory syncytial virus (RSV) poses a significant public health threat, particularly to children and the elderly. Two protein-based vaccines and one mRNA vaccine have been approved, all targeting the prefusion conformation of the fusion (F) trimer. However, it has been reported that the epitope activity of the F protein gradually declines during storage, resulting in a reduction of the vaccines' immunogenicity.
View Article and Find Full Text PDFProtein Sci
September 2025
Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich, Germany.
The pyrroloindole (hexahydropyrrolo[2,3-b]indole, HPI) structural motif is present in a wide range of natural products with various biological activities, yet its chemical synthesis poses a challenge, particularly regarding methylation at the indole C3 position. In nature, S-adenosyl methionine (SAM)-dependent methyltransferases efficiently catalyze this reaction with high stereoselectivity. This study presents the investigation and rational re-design of a potential methyltransferase, termed SeMT, from the actinomycete Saccharopolyspora erythraea.
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